No abstract
The thale cress Arabidopsis thaliana is a powerful model organism for studying a wide variety of biological processes. Recent advances in sequencing technology have resulted in a wealth of information describing numerous aspects of A. thaliana genome function. However, there is a relative paucity of computational systems for efficiently and effectively using these data to create testable hypotheses. We present CressInt, a user-friendly web resource for exploring gene regulatory mechanisms in A. thaliana on a genomic scale. The CressInt system incorporates a variety of genome-wide data types relevant to gene regulation, including transcription factor (TF) binding site models, ChIP-seq, DNase-seq, eQTLs, and GWAS. We demonstrate the utility of CressInt by showing how the system can be used to (1) Identify TFs binding to the promoter of a gene of interest; (2) identify genetic variants that are likely to impact TF binding based on a ChIP-seq dataset; and (3) identify specific TFs whose binding might be impacted by phenotype-associated variants. CressInt is freely available at http://cressint.cchmc.org.
Eosinophils develop in the bone marrow from hematopoietic progenitors into mature cells capable of a plethora of immunomodulatory roles via the choreographed process of eosinophilopoiesis. However, the gene regulatory elements and transcription factors (TFs) orchestrating this process remain largely unknown. The potency and resulting diversity fundamental to an eosinophil’s complex immunomodulatory functions and tissue specialization likely result from dynamic epigenetic regulation of the eosinophil genome, a dynamic eosinophil regulome. In this study, we applied a global approach using broad-range, next-generation sequencing to identify a repertoire of eosinophil-specific enhancers. We identified over 8200 active enhancers located within 1–20 kB of expressed eosinophil genes. TF binding motif analysis revealed PU.1 (Spi1) motif enrichment in eosinophil enhancers, and chromatin immunoprecipitation coupled with massively parallel sequencing confirmed PU.1 binding in likely enhancers of genes highly expressed in eosinophils. A substantial proportion (>25%) of these PU.1-bound enhancers were unique to murine, culture-derived eosinophils when compared among enhancers of highly expressed genes of three closely related myeloid cell subsets (macrophages, neutrophils, and immature granulocytes). Gene ontology analysis of eosinophil-specific, PU.1-bound enhancers revealed enrichment for genes involved in migration, proliferation, degranulation, and survival. Furthermore, eosinophil-specific superenhancers were enriched in genes whose homologs are associated with risk loci for eosinophilia and allergic diseases. Our collective data identify eosinophil-specific enhancers regulating key eosinophil genes through epigenetic mechanisms (H3K27 acetylation) and TF binding (PU.1).
setts General Hospital. RATIONALE: Dendritic cells (DCs) are innate immune sentinels. Upon encounter with pathogens, they mature and migrate to draining lymph nodes (dLNs), where they can initiate adaptive immune responses. The process by which Th2 immunogens lead to this response is unclear. We recently showed that Th2-skewing CD301b + DCs upregulate CCR8 after allergen stimulation in na€ ıve mice, which was required for DCs entry into the dLN parenchyma and subsequent Th2 responses. This was dependent on production of the CCR8 ligand, CCL8, by interfollicular region macrophages (IFR macs). Thus, IFR macrophages likely have the ability to remotely sense Th2 immunogens. In this study, we capitalized on the allergen-sensing ability of IFR macs to identify mechanisms of Th2 immunogen sensing. METHODS: IFR macs were enriched using magnetic-activated cell sorting of SIGN-R1 + cells in digested lymph nodes. Bone marrow-derived macrophages (BMDMs) were generated from C57Bl/6 mice. RNASeq analysis and QPCR was performed to assess gene expression. RESULTS: IFR macs and BMDMs treated in vitro with papain and other cysteine protease immunogens upregulated Ccl8, while treatment with LPS did not. Papain-induced Ccl8 expression was dependent on serum, although supplementation of media with gamma globulin or albumin alone was not permissive for papain-induced Ccl8 epxression. RNA-seq analysis of BMDMs treated with papain demonstrated multiple differentially-regulated pathways. CONCLUSIONS: Macrophages produced Ccl8 directly in response to cysteine protease allergens in a serum-dependent fashion. This suggests that papain is sensed by a serum component, which is recognized by macrophages. Transcriptomic analysis gives clues to the mechanisms by which this occurs.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
customersupport@researchsolutions.com
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.